From 9d6cde36b08d66dca8a7c0eb0aff18a1c7e97e3b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Oct 2021 15:55:54 +0200
Subject: [PATCH] danpos: simplify bg2wig import
---
src/nf_modules/danpos/main.nf | 21 +++++++--------------
1 file changed, 7 insertions(+), 14 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index fda86102..ece0991b 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -2,8 +2,7 @@ version = "v2.2.2_cv3"
container_url = "biocontainers/danpos:${version}"
include {
- bigwig_to_wig as bigwig_to_wig_ip;
- bigwig_to_wig_ip as bigwig_to_wig_wce
+ bigwig_to_wig
} from "./../ucsc/main.nf"
params.dpos = "--smooth_width 0 -n N "
@@ -59,9 +58,7 @@ workflow dpos_bg {
bg_ip
bg_wce
main:
- bigwig_to_wig_ip(bg_ip)
- bigwig_to_wig_wce(bg_wce)
- dpos_wig(fastq, bigwig_to_wig_ip.out.wig, bigwig_to_wig_wce.out.wig)
+ dpos_wig(fastq, bigwig_to_wig(bg_ip), bigwig_to_wig(bg_wce))
emit:
wig = dpos_wig.out.wig
folder = dpos_wig.out.folder
@@ -210,9 +207,7 @@ workflow dpeak_bg {
bg_ip
bg_wce
main:
- bigwig_to_wig_ip(bg_ip)
- bigwig_to_wig_wce(bg_wce)
- dpeak_wig(fastq, bigwig_to_wig_ip.out.wig, bigwig_to_wig_wce.out.wig)
+ dpeak_wig(fastq, bigwig_to_wig(bg_ip), bigwig_to_wig(bg_wce))
emit:
wig = dpeak_wig.out.wig
folder = dpeak_wig.out.folder
@@ -270,14 +265,12 @@ workflow dpeak_bgvsbg {
bg_ip_b
bg_wce_b
main:
- bigwig_to_wig_ip(bg_ip)
- bigwig_to_wig_wce(bg_wce)
dpeak_wigvswig(
fastq,
- bigwig_to_wig_ip(bg_ip_a).out.wig,
- bigwig_to_wig_wce(bg_wce_a).out.wig,
- bigwig_to_wig_ip(bg_ip_b).out.wig,
- bigwig_to_wig_wce(bg_wce_b).out.wig
+ bigwig_to_wig(bg_ip_a),
+ bigwig_to_wig(bg_wce_a),
+ bigwig_to_wig(bg_ip_b),
+ bigwig_to_wig(bg_wce_b)
)
emit:
wig = dpeak_wig.out.wig
--
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